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Farzi R, Pirbonyeh N, Kadivar MR, Moattari A. Prevalence of Influenza Viruses A and B, Adenovirus, Respiratory Syncytial Virus, and Human Metapneumonia Viruses among Children with Acute Respiratory Tract Infection. Adv Virol 2024; 2024:7613948. [PMID: 38292215 PMCID: PMC10824580 DOI: 10.1155/2024/7613948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/04/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Background Acute respiratory tract infection (ARTI) is a significant cause of morbidity and mortality among children worldwide. The majority of acute respiratory infections in children are caused by viruses, with respiratory syncytial virus (RSV) being the most frequently encountered. Other important viral pathogens include human metapneumovirus, human coronaviruses, adenovirus, and influenza. These infections can lead to complications such as bronchitis and pneumonia. So, this study aimed to evaluate the prevalence of influenza viruses A and B, adenovirus, respiratory syncytial virus (RSV), and human metapneumovirus (HMPV) in children with ARTI. Methods The molecular diagnostic of polymerase chain reaction approach was used to detect influenza (A and B), metapneumovirus, respiratory syncytial virus (RSV), and adenovirus in respiratory samples of children with acute respiratory infection hospitalization in a teaching hospital of the Shiraz University of Medical Sciences in January 2016-March 2017. Results Of the 340 patients examined, 208 (61.20%) were male and the median age was 3.13 ± 2.38 years. Respiratory viruses were found in 179 (52.64%) patients. The male-to-female ratio was 1.63 : 1 in patients who were viral positive. Detection rates for influenza A, adenovirus, influenza B, RSV, and HMPV were 28.23%, 24.70%, 8.52%, 3.23%, and 2.64%, respectively, and coinfections were detected in 24.02%. The most common combination of two-virus coinfections was IFVA/AdV, followed by IFVB/AdV, AdV, IFVB/IFVA, RSV/IFVA, HMPV/AdV, RSV/AdV, and HMPV/IFVA. Conclusion The high prevalence of respiratory viruses in children hospitalized with ARTI suggests that viral infection may play a role in disease pathogenesis. This should be confirmed through the conduct of case-control studies and may inform the role of vaccination to prevent respiratory viral infections.
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Affiliation(s)
- Rana Farzi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Pirbonyeh
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Burn and Wound Healing Research Center, Microbiology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Rahim Kadivar
- Department of Pediatrics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Professor Alborzi Clinical Microbiology Research Center, Namazi Hospital, Shiraz Medical University, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Xiang WQ, Li L, Guo YJ, Lin J, Li W. The Impact of COVID-19 Public Health Measures on Detection of Other Respiratory Viruses in Children during the Winter of 2020–2021 in Hangzhou, China. J PEDIAT INF DIS-GER 2022. [DOI: 10.1055/s-0042-1756712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
Abstract
Objective Acute respiratory tract infection (ARTI) is one of the main diseases in childhood. This study aimed to monitor the distribution of respiratory tract viruses in children with ARTI in the impact of coronavirus disease 2019 (COVID-19).
Methods We conducted surveillance of 2019 novel coronavirus, human metapneumovirus, respiratory syncytial virus, human adenovirus, human parainfluenza virus 1–3, and influenza A and B virus by using quantitative real-time polymerase chain reaction.
Results During the winter of 2020 to 2021, among the 1,442 throat swabs we collected, 937 (64.98%, 937/1,442) were positive for respiratory viruses. Respiratory syncytial virus was the most frequently detected respiratory virus (34.12%, 492/1,442) and 2019 novel coronavirus and influenza A and B virus were not detected in the study period. Coinfection was observed in 156 positive samples including 149 samples of double infection and 7 of triple infection. The positive rate of viral respiratory tract infection in infants less than 6 months was the highest (72.95%) in the study period.
Conclusion There are some differences in the distribution of respiratory viruses in children after the outbreak of COVID-19 in Hangzhou, China.
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Affiliation(s)
- Wen-qing Xiang
- Department of Clinical Laboratory, The Children's Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, P.R. China
| | - Lin Li
- Department of Clinical Laboratory, The Children's Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, P.R. China
| | - Ya-jun Guo
- Department of Clinical Laboratory, The Children's Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, P.R. China
| | - Jian Lin
- Department of Clinical Laboratory, The Children's Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, P.R. China
| | - Wei Li
- Department of Clinical Laboratory, The Children's Hospital, National Clinical Research Center For Child Health, Zhejiang University School of Medicine, Hangzhou, P.R. China
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Johnson EK, Sylte D, Chaves SS, Li Y, Mahe C, Nair H, Paget J, van Pomeren T, Shi T, Viboud C, James SL. Hospital utilization rates for influenza and RSV: a novel approach and critical assessment. Popul Health Metr 2021; 19:31. [PMID: 34126993 PMCID: PMC8204427 DOI: 10.1186/s12963-021-00252-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/31/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Influenza and respiratory syncytial virus (RSV) contribute significantly to the burden of acute lower respiratory infection (ALRI) inpatient care, but heterogeneous coding practices and availability of inpatient data make it difficult to estimate global hospital utilization for either disease based on coded diagnoses alone. METHODS This study estimates rates of influenza and RSV hospitalization by calculating the proportion of ALRI due to influenza and RSV and applying this proportion to inpatient admissions with ALRI coded as primary diagnosis. Proportions of ALRI attributed to influenza and RSV were extracted from a meta-analysis of 360 total sources describing inpatient hospital admissions which were input to a Bayesian mixed effects model over age with random effects over location. Results of this model were applied to inpatient admission datasets for 44 countries to produce rates of hospital utilization for influenza and RSV respectively, and rates were compared to raw coded admissions for each disease. RESULTS For most age groups, these methods estimated a higher national admission rate than the rate of directly coded influenza or RSV admissions in the same inpatient sources. In many inpatient sources, International Classification of Disease (ICD) coding detail was insufficient to estimate RSV burden directly. The influenza inpatient burden estimates in older adults appear to be substantially underestimated using this method on primary diagnoses alone. Application of the mixed effects model reduced heterogeneity between countries in influenza and RSV which was biased by coding practices and between-country variation. CONCLUSIONS This new method presents the opportunity of estimating hospital utilization rates for influenza and RSV using a wide range of clinical databases. Estimates generally seem promising for influenza and RSV associated hospitalization, but influenza estimates from primary diagnosis seem highly underestimated among older adults. Considerable heterogeneity remains between countries in ALRI coding (i.e., primary vs non-primary cause), and in the age profile of proportion positive for influenza and RSV across studies. While this analysis is interesting because of its wide data utilization and applicability in locations without laboratory-confirmed admission data, understanding the sources of variability and data quality will be essential in future applications of these methods.
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Affiliation(s)
- Emily K Johnson
- Institute of Health Metrics and Evaluation, University of Washington, Seattle, USA.
| | - Dillon Sylte
- Institute of Health Metrics and Evaluation, University of Washington, Seattle, USA
| | - Sandra S Chaves
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
- Vaccine Epidemiology and Modeling Department, Sanofi Pasteur, Lyon, France
| | - You Li
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Cedric Mahe
- Foundation for Influenza Epidemiology, Fondation de France, Paris, France
- Vaccine Epidemiology and Modeling Department, Sanofi Pasteur, Lyon, France
| | - Harish Nair
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - John Paget
- Netherlands Institute for Health Services Research (Nivel), Utrecht, Netherlands
| | - Tayma van Pomeren
- Netherlands Institute for Health Services Research (Nivel), Utrecht, Netherlands
| | - Ting Shi
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Cecile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, USA
| | - Spencer L James
- Institute of Health Metrics and Evaluation, University of Washington, Seattle, USA
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Deberu O, Nkrumah B, Sylverken AA, Sambian D, Acheampong G, Amuasi J, Stebleson A, Agboyie D, Yenbaree M, Mensah S, Dombadoh A, Owusu DO, Abdul-Karim A, Owusu M. Common bacteria in sputum or gastric lavage of patients presenting with signs and symptoms of lower respiratory tract infections. Pan Afr Med J 2021; 38:383. [PMID: 34381527 PMCID: PMC8325465 DOI: 10.11604/pamj.2021.38.383.26333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/08/2021] [Indexed: 11/11/2022] Open
Abstract
Introduction lower respiratory tract infections (LRTIs) are infections involving the trachea, primary bronchi and lungs. People with LRTIs typically experience coughs as the primary symptoms; however, shortness of breath, weakness, fever and fatigue may be coupled with the cough. It is common among the aged, children under five and the immune-suppressed. Persons with symptoms suggestive of pulmonary tuberculosis (TB) may have tuberculosis, other respiratory tract infection or co-infection of tuberculosis and other respiratory pathogens. This study aimed to identify the presence of pathogens in sputum of suspected tuberculosis cases and their antimicrobial resistance patterns. Methods this was a retrospective study conducted from September 2018 to November 2019 at Tamale Public Health Laboratory. Sputum or gastric lavage samples were collected from persons with suspected clinical presentations of TB and/or LRTI. These samples were cultured using standard microbiological protocols and antimicrobial susceptibility test performed on the positive cultures by Kirby-Bauer disc diffusion method. Molecular identification of M. tuberculosis was performed on all the suspected TB cases using GeneXpert mycobacterium tuberculosis/rifampin (MTB/RIF) assay. Results during the study period, there were 264 cases of which 49.2% were males and 50.8% were females. Positive cases for culture were 47.3%. Out of the 264 cases, 186 (70.5%) were suspected TB with 51.6% being positive for culture, 6.5% positive for M. tuberculosis (GeneXpert confirmed) and 3.8% co-infection of TB with other bacteria pathogens. Klebsiella spp. (35/125; 28%) and Pseudomonas spp. (19/125; 15.2%) were the most predominant pathogens isolated. There was no significant difference in detection of bacteria in males and females (p=0.89), however individuals with suspected TB were significantly infected with other bacterial species than the unsuspected individuals (p=0.03). Almost all the isolates showed high susceptibility towards carbapenem (meropenem) and high resistance towards the third generation cephalosporins (cefotaxime and ceftriaxone). Conclusion this study highlights the need to test individuals with classical symptoms of LRTIs for other bacterial infections other than TB only. Sputum culture is recommended for all suspected tuberculosis cases to provide accurate laboratory diagnosis to LRTIs and mitigate unnecessary use of antimicrobials.
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Affiliation(s)
- Oliver Deberu
- Tamale Public Health Laboratory, Tamale, Ghana.,Centre for Health Systems Strengthening, Kumasi, Ghana
| | | | - Augustina Angelina Sylverken
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - David Sambian
- Centre for Health Systems Strengthening, Kumasi, Ghana
| | | | - John Amuasi
- Department of Global Health, School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | | | | | | | | | | | - Michael Owusu
- Centre for Health Systems Strengthening, Kumasi, Ghana.,Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Li J, Song CL, Wang T, Ye YL, Du JR, Li SH, Zhu JM. Etiological and epidemiological characteristics of severe acute respiratory infection caused by multiple viruses and Mycoplasma pneumoniae in adult patients in Jinshan, Shanghai: A pilot hospital-based surveillance study. PLoS One 2021; 16:e0248750. [PMID: 33750952 PMCID: PMC7984646 DOI: 10.1371/journal.pone.0248750] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
Background Severe acute respiratory infection (SARI) results in a tremendous disease burden worldwide. Available research on active surveillance among hospitalized adult patients suffering from SARI in China is limited. This pilot study aimed to identify associated etiologies and describe the demographic, epidemiological and clinical profiles of hospitalized SARI patients aged over 16 years in Jinshan, Shanghai. Methods Active surveillance was conducted at 1 sentinel hospital in Jinshan district, Shanghai, from April 2017 to March 2018. Hospitalized SARI patients aged over 16 years old were enrolled, and nasopharyngeal swabs were collected within 24 hours of admission and tested for multiple respiratory viruses (including 18 common viruses) and Mycoplasma pneumoniae with real-time polymerase chain reaction. Demographic, epidemiological and clinical information was obtained from case report forms. Results In total, 397 SARI patients were enrolled; the median age was 68 years, and 194 (48.9%) patients were male. A total of 278 (70.0%) patients had at least one underlying chronic medical condition. The most frequent symptoms were cough (99.2%) and sputum production (88.4%). The median duration of hospitalization was 10 days. A total of 250 infection patients (63.0%) were positive for at least one pathogen, of whom 198 (49.9%) were positive for a single pathogen and 52 (13.1%) were positive for multiple pathogens. The pathogens identified most frequently were M. pneumoniae (23.9%, 95/397), followed by adenovirus (AdV) (11.6%, 46/397), influenza virus A/H3N2 (Flu A/H3N2) (11.1%, 44/397), human rhinovirus (HRhV) (8.1%, 32/397), influenza virus B/Yamagata (Flu B/Yamagata) (6.3%, 25/397), pandemic influenza virus A/H1N1 (Flu A/pH1N1) (4.0%, 16/397), parainfluenza virus (PIV) type 1 (2.0%, 8/397), human coronavirus (HCoV) type NL63 (2.0%, 8/397), HCoV 229E (1.5%, 6/397), HCoV HKU1 (1.5%, 6/397), PIV 3 (1.5%, 6/397), human metapneumovirus (HMPV) (1.5%, 6/397), PIV 4 (1.3%, 5/397), HCoV OC43 (1.0%, 4/397), influenza virus B/Victoria (Flu B/Victoria) (0.5%, 2/397), respiratory syncytial virus (RSV) type B (0.5%, 2/397), and human bocavirus (HBoV) (0.3%, 1/397). The seasonality of pathogen-confirmed SARI patients had a bimodal distribution, with the first peak in the summer and the second peak in the winter. Statistically significant differences were observed with respect to the rates of dyspnea, radiographically diagnosed pneumonia and the presence of at least one comorbidity in patients who were infected with only M. pneumoniae, AdV, HRhV, Flu A/H3N2, Flu A /pH1N1 or Flu B/Yamagata. The differences in the positivity rates of the above 6 pathogens among the different age groups were nonsignificant. Conclusions M. pneumoniae, AdV and Flu A/H3N2 were the main pathogens detected in hospitalized SARI patients aged over 16 years old in Jinshan district, Shanghai. Our findings highlight the importance of sustained multipathogen surveillance among SARI patients in sentinel hospitals, which can provide useful information on SARI etiologies, epidemiology, and clinical characteristics.
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Affiliation(s)
- Jian Li
- Clinical Research Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (JL); (JMZ)
| | - Can-Lei Song
- Department of Acute Infectious Diseases Control, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
| | - Tang Wang
- Department of Acute Infectious Diseases Control, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
| | - Yu-Long Ye
- Department of Microbiology, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
| | - Jian-Ru Du
- Department of Microbiology, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
| | - Shu-Hua Li
- Department of Acute Infectious Diseases Control, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
| | - Jian-Min Zhu
- Department of Acute Infectious Diseases Control, Jinshan District Center for Diseases Control and Prevention, Shanghai, China
- * E-mail: (JL); (JMZ)
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DeFelice T. Relationship between temporal anomalies in PM 2.5 concentrations and reported influenza/influenza-like illness activity. Heliyon 2020; 6:e04726. [PMID: 32835121 PMCID: PMC7428445 DOI: 10.1016/j.heliyon.2020.e04726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/06/2020] [Accepted: 08/11/2020] [Indexed: 12/20/2022] Open
Abstract
A small number of studies suggest atmospheric particulate matter with diameters 2.5 micron and smaller (PM2.5) may possibly play a role in the transmission of influenza and influenza-like illness (ILI) symptoms. Those studies were predominantly conducted under moderately to highly polluted outdoor atmospheres. The purpose of this study was to extend the data set to include a less polluted atmospheric environment. A relationship between PM2.5 and ILI activity extended to include lightly to moderately polluted atmospheres could imply a more complicated mechanism than that suggested by existing studies. We obtained concurrent PM2.5 mass concentration data, meteorological data and reported Influenza and influenza-like illness (ILI) activity for the light to moderately polluted atmospheres over the Tucson, AZ region. We found no relation between PM2.5 mass concentration and ILI activity. There was an expected relation between ILI, activity, temperature, and relative humidity. There was a possible relation between PM2.5 mass concentration anomalies and ILI activity. These results might be due to the small dataset size and to the technological limitations of the PM measurements. Further study is recommended since it would improve the understanding of ILI transmission and thereby improve ILI activity/outbreak forecasts and transmission model accuracies.
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Abstract
Respiratory syncytial virus (RSV) is the most common pathogen associated with acute lower respiratory tract infections in young children. RSV is also a major viral pathogen causing severe lung disease in the adult population, particularly among the elderly. We conducted a review of adult RSV studies published from January 1970 to February 2017 to determine the burden of disease among adults worldwide. There were no restrictions on health care setting or definition of RSV infection. A total of 1530 published studies were identified, 95 of which were included in this review. The incidence rates of hospitalised RSV acute respiratory tract infection (ARI) in adults >65 years old ranged from 7.3 to 13.0/105 population in Africa and Asia and from 190 to 254/105 population in the USA. Higher incidence rates (195–1790/105 population) were observed in adults ≥50 years old for outpatient or emergency visits in the USA. Of all ARI patients, RSV accounted for 1–10% in adults and 2–14% in patients with chronic diseases or transplantation. Given the limitations in the existing data, significant efforts should be made to generate evidence on the burden of RSV infections in adults and to estimate the potential impact of future preventive interventions.
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Liu W, Dai Q, Bao J, Shen W, Wu Y, Shi Y, Xu K, Hu J, Bao C, Huo X. Influenza activity prediction using meteorological factors in a warm temperate to subtropical transitional zone, Eastern China. Epidemiol Infect 2019; 147:e325. [PMID: 31858924 PMCID: PMC7006024 DOI: 10.1017/s0950268819002140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/21/2019] [Accepted: 11/27/2019] [Indexed: 11/12/2022] Open
Abstract
Influenza activity is subject to environmental factors. Accurate forecasting of influenza epidemics would permit timely and effective implementation of public health interventions, but it remains challenging. In this study, we aimed to develop random forest (RF) regression models including meterological factors to predict seasonal influenza activity in Jiangsu provine, China. Coefficient of determination (R2) and mean absolute percentage error (MAPE) were employed to evaluate the models' performance. Three RF models with optimum parameters were constructed to predict influenza like illness (ILI) activity, influenza A and B (Flu-A and Flu-B) positive rates in Jiangsu. The models for Flu-B and ILI presented excellent performance with MAPEs <10%. The predicted values of the Flu-A model also matched the real trend very well, although its MAPE reached to 19.49% in the test set. The lagged dependent variables were vital predictors in each model. Seasonality was more pronounced in the models for ILI and Flu-A. The modification effects of the meteorological factors and their lagged terms on the prediction accuracy differed across the three models, while temperature always played an important role. Notably, atmospheric pressure made a major contribution to ILI and Flu-B forecasting. In brief, RF models performed well in influenza activity prediction. Impacts of meteorological factors on the predictive models for influenza activity are type-specific.
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Affiliation(s)
- Wendong Liu
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Qigang Dai
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jing Bao
- Jiangsu Meteorological Service Center, Nanjing, China
| | - Wenqi Shen
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Ying Wu
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Yingying Shi
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Ke Xu
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Jianli Hu
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Changjun Bao
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Xiang Huo
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
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Bacterial Aetiologies of Lower Respiratory Tract Infections among Adults in Yaoundé, Cameroon. BIOMED RESEARCH INTERNATIONAL 2019; 2019:4834396. [PMID: 31119172 PMCID: PMC6500673 DOI: 10.1155/2019/4834396] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/28/2019] [Accepted: 04/11/2019] [Indexed: 02/06/2023]
Abstract
Lower respiratory tract infections (LRTIs) remain a challenge in African healthcare settings and only few data are available on their aetiology in Cameroon. The purpose of this study was to access the bacterial cause of LRTIs in patients in Cameroon by two methods. Methods. Participants with LRTIs were enrolled in the referral centre for respiratory diseases in Yaoundé city and its surroundings. To detect bacteria, specimens were tested by conventional bacterial culture and a commercial reverse-transcriptase real-time polymerase chain reaction (RT-PCR) assay. One hundred forty-one adult patients with LRTIs were enrolled in the study. Among the participants, 46.8% were positive for at least one bacterium. Streptococcus pneumoniae and Haemophilus influenzae were the most detected bacteria with 14.2% (20/141) followed by Klebsiella pneumoniae, 9.2% (13/141), Staphylococcus aureus, 7.1% (10/141), and Moraxella catarrhalis, 4.3% (6/141). Bacterial coinfection accounted for 23% (14/61) with Haemophilus influenzae being implicated in 19.7% (12/61). The diagnostic performance of RT-PCR for bacteria detection (43.3%) was significantly different from that of culture (17.7%) (p< 0.001). Only Streptococcus pneumoniae detection was associated with empyema by RT-PCR (p<0.001). These findings enhance understanding of bacterial aetiologies in order to improve respiratory infection management and treatment. It also highlights the need to implement molecular tools as part of the diagnosis of LRTIs.
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Kurskaya O, Ryabichenko T, Leonova N, Shi W, Bi H, Sharshov K, Kazachkova E, Sobolev I, Prokopyeva E, Kartseva T, Alekseev A, Shestopalov A. Viral etiology of acute respiratory infections in hospitalized children in Novosibirsk City, Russia (2013 - 2017). PLoS One 2018; 13:e0200117. [PMID: 30226876 PMCID: PMC6143185 DOI: 10.1371/journal.pone.0200117] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/04/2018] [Indexed: 12/14/2022] Open
Abstract
Background Acute respiratory infections (ARIs) cause a considerable morbidity and mortality worldwide especially in children. However, there are few studies of the etiological structure of ARIs in Russia. In this work, we analyzed the etiology of ARIs in children (0–15 years old) admitted to Novosibirsk Children’s Municipal Clinical Hospital in 2013–2017. Methods We tested nasal and throat swabs of 1560 children with upper or lower respiratory infection for main respiratory viruses (influenza viruses A and B, parainfluenza virus types 1–4, respiratory syncytial virus, metapneumovirus, four human coronaviruses, rhinovirus, adenovirus and bocavirus) using a RT-PCR Kit. Results We detected 1128 (72.3%) samples were positive for at least one virus. The most frequently detected pathogens were respiratory syncytial virus (358/1560, 23.0%), influenza virus (344/1560, 22.1%), and rhinovirus (235/1560, 15.1%). Viral co-infections were found in 163 out of the 1128 (14.5%) positive samples. We detected significant decrease of the respiratory syncytial virus-infection incidence in children with increasing age, while the reverse relationship was observed for influenza viruses. Conclusions We evaluated the distribution of respiratory viruses in children with ARIs and showed the prevalence of respiratory syncytial virus and influenza virus in the etiological structure of infections. This study is important for the improvement and optimization of diagnostic tactics, control and prevention of the respiratory viral infections.
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Affiliation(s)
- Olga Kurskaya
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
- * E-mail:
| | - Tatyana Ryabichenko
- Department of Propaedeutic of Childhood Diseases, Novosibirsk State Medical University, Novosibirsk, Russia
| | - Natalya Leonova
- Department of Children’s Diseases, Novosibirsk Children’s Municipal Clinical Hospital №6, Novosibirsk, Russia
| | - Weifeng Shi
- Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Taishan Medical College, Taian, Shandong, China
| | - Hongtao Bi
- Qinghai Key Laboratory of Tibetan Medicine Pharmacology and Safety Evaluation, Northwest Institute of Plateau Biology, CAS, Xining, China
| | - Kirill Sharshov
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Eugenia Kazachkova
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Ivan Sobolev
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Elena Prokopyeva
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Tatiana Kartseva
- Department of Propaedeutic of Childhood Diseases, Novosibirsk State Medical University, Novosibirsk, Russia
| | - Alexander Alekseev
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Alexander Shestopalov
- Department of Experimental Modeling and Pathogenesis of Infectious Diseases, Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
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Ma W, Huo X, Zhou M. The healthcare seeking rate of individuals with influenza like illness: a meta-analysis. Infect Dis (Lond) 2018; 50:728-735. [PMID: 30009680 DOI: 10.1080/23744235.2018.1472805] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
BACKGROUND Not all individuals with Influenza like illness (ILI) seek healthcare. Knowing the proportion that do is important to evaluate the actual burden and fatality rate of ILI-relevant diseases, such as seasonal influenza and human infection with avian influenza. A number of studies have investigated the healthcare seeking rate, but the results varied from 0.16 to 0.85. We conducted this analysis for better understanding the healthcare seeking rate for ILI, and providing fundamental data for researchers in relevant fields. METHODS In this meta-analysis, a total of 799 articles, published as of 13 December 2016, were retrieved from Pubmed, Embase, Web of Science and Cochrane, and 11 of them were included after screening. The pooled estimates and factors which influence healthcare seeking rates were analysed. RESULTS The overall pooled healthcare seeking rate was 0.52 (95% CI: 0.46-0.59). The rate was significantly higher during the H1N1 pandemic in 2009 (0.61, 95% CI: 0.51-0.74), in children (0.56, 95% CI: 0.55-0.57) and in patients with documented fever (0.62, 95% CI: 0.53-0.72) than during non-pandemic periods (0.39, 95% CI: 0.33-0.45), in adults (0.45, 95% CI: 0.42-0.48) and in patients without documented fever (0.44, 95% CI: 0.38-0.50). Meta-regression indicated that these three factors could jointly explain 70.1% of the total heterogeneity among published studies. CONCLUSION The healthcare seeking rate of ILI patients is needed for estimation of the burden of ILI in the general population based on data from routine ILI sentinel surveillance systems.
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Affiliation(s)
- Wang Ma
- a School of Public Health , Nanjing Medical University , Nanjing , China
| | - Xiang Huo
- b Jiangsu Provincial Center for Disease Control and Prevention , Nanjing , China
| | - Minghao Zhou
- a School of Public Health , Nanjing Medical University , Nanjing , China.,b Jiangsu Provincial Center for Disease Control and Prevention , Nanjing , China
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12
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Jennings L, Huang QS, Barr I, Lee PI, Kim WJ, Buchy P, Sanicas M, Mungall BA, Chen J. Literature review of the epidemiology of influenza B disease in 15 countries in the Asia-Pacific region. Influenza Other Respir Viruses 2018; 12:383-411. [PMID: 29127742 PMCID: PMC5907823 DOI: 10.1111/irv.12522] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2017] [Indexed: 01/06/2023] Open
Abstract
Influenza control strategies focus on the use of trivalent influenza vaccines containing two influenza A virus subtypes and one of the two circulating influenza type B lineages (Yamagata or Victoria). Mismatches between the vaccine B lineage and the circulating lineage have been regularly documented in many countries, including those in the Asia‐Pacific region. We conducted a literature review with the aim of understanding the relative circulation of influenza B viruses in Asia‐Pacific countries. PubMed and Western Pacific Region Index Medicus were searched for relevant articles on influenza type B published since 1990 in English language for 15 Asia‐Pacific countries. Gray literature was also accessed. From 4834 articles identified, 121 full‐text articles were analyzed. Influenza was reported as an important cause of morbidity in the Asia‐Pacific region, affecting all age groups. In all 15 countries, influenza B was identified and associated with between 0% and 92% of laboratory‐confirmed influenza cases in any one season/year. Influenza type B appeared to cause more illness in children aged between 1 and 10 years than in other age groups. Epidemiological data for the two circulating influenza type B lineages remain limited in several countries in the Asia‐Pacific, although the co‐circulation of both lineages was seen in countries where strain surveillance data were available. Mismatches between circulating B lineages and vaccine strains were observed in all countries with available data. The data suggest that a shift from trivalent to quadrivalent seasonal influenza vaccines could provide additional benefits by providing broader protection.
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Affiliation(s)
- Lance Jennings
- Canterbury District Health Board, Christchurch, New Zealand
| | - Qiu Sue Huang
- WHO National Influenza Centre, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, VIC, Australia
| | - Ping-Ing Lee
- Department of Pediatrics, National Taiwan University Children's Hospital, Taipei, Taiwan
| | - Woo Joo Kim
- Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea
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13
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Zheng X, Song Z, Li Y, Zhang J, Wang XL. Possible interference between seasonal epidemics of influenza and other respiratory viruses in Hong Kong, 2014-2017. BMC Infect Dis 2017; 17:772. [PMID: 29246199 PMCID: PMC5732536 DOI: 10.1186/s12879-017-2888-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 12/06/2017] [Indexed: 12/03/2022] Open
Abstract
Background Unlike influenza viruses, little is known about the prevalence and seasonality of other respiratory viruses because laboratory surveillance for non-influenza respiratory viruses is not well developed or supported in China and other resource-limited countries. We studied the interference between seasonal epidemics of influenza viruses and five other common viruses that cause respiratory illnesses in Hong Kong from 2014 to 2017. Methods The weekly laboratory-confirmed positive rates of each virus were analyzed from 2014 to 2017 in Hong Kong to describe the epidemiological trends and interference between influenza viruses, respiratory syncytial virus (RSV), parainfluenza virus (PIV), adenovirus, enterovirus and rhinovirus. A sinusoidal model was established to estimate the peak timing of each virus by phase angle parameters. Results Seasonal features of the influenza viruses, PIV, enterovirus and adenovirus were obvious, whereas annual peaks of RSV and rhinovirus were not observed. The incidence of the influenza viruses usually peaked in February and July, and the summer peaks in July were generally caused by the H3 subtype of influenza A alone. When influenza viruses were active, other viruses tended to have a low level of activity. The peaks of the influenza viruses were not synchronized. An epidemic of rhinovirus tended to shift the subsequent epidemics of the other viruses. Conclusion The evidence from recent surveillance data in Hong Kong suggests that viral interference during the epidemics of influenza viruses and other common respiratory viruses might affect the timing and duration of subsequent epidemics of a certain or several viruses.
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Affiliation(s)
- Xueying Zheng
- Department of Biostatistics and Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China.,Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China
| | - Zhengyu Song
- Department of Biostatistics and Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Yapeng Li
- Department of Biostatistics and Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Juanjuan Zhang
- Department of Biostatistics and Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Xi-Ling Wang
- Department of Biostatistics and Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China. .,Collaborative Innovation Center of Social Risks Governance in Health, Fudan University, Shanghai, China. .,Shanghai Key Laboratory of Meteorology and Health, Shanghai, China.
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14
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Respiratory Tract Viral Infections and Coinfections Identified by Anyplex™ II RV16 Detection Kit in Pediatric Patients at a Riyadh Tertiary Care Hospital. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1928795. [PMID: 29359144 PMCID: PMC5735607 DOI: 10.1155/2017/1928795] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/07/2017] [Accepted: 10/08/2017] [Indexed: 02/03/2023]
Abstract
Respiratory infections are caused by an array of viruses, and limited information is available about viral coexistence, comparative symptoms, and the burden of illness. This retrospective cohort study aimed to determine the etiological agents responsible for respiratory tract infections by Anyplex II RV16 detection kit (RV16, Seegene), involving 2266 pediatric patients with respiratory infections admitted to the Department of Pediatrics at King Abdul-Aziz Medical City, Ministry of National Guard, Riyadh, from July 2014 to June 2015. The most frequent respiratory infections were recorded in the 1 to 5 year age group (44.7%). Rhinovirus (32.5%), Adenovirus (16.9%), and Respiratory syncytial virus (RSV) B (10.4%) were most common. In single viral infections, Rhinovirus (41.2%), Metapneumovirus (15.3%), and Bocavirus (13.7%) were most frequent. In multiple viral infections, Rhinovirus (36.7%), Adenovirus (35.2%), Bocavirus (11.2), RSV B (7.8%), and RSV A (6.7%) were most frequent. No significant difference was observed in clinical presentations; however, rhinorrhea and hypodynamia were significantly associated with viral respiratory infections. Most respiratory viral pathogens peaked during December, January, March, and April. Rhinovirus, Adenovirus, and Bocavirus circulations were detected throughout the year. Winter peaks were recorded for Rhinovirus, RSV B, Adenovirus, and RSV A, whereas the Metapneumovirus, and the Bocavirus peaked in March and April. These findings enhance understanding of viral etiology and distribution to improve respiratory infection management and treatment.
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15
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Ye C, Zhu W, Yu J, Li Z, Fu Y, Lan Y, Lai S, Wang Y, Pan L, Sun Q, Zhao G. Viral pathogens among elderly people with acute respiratory infections in Shanghai, China: Preliminary results from a laboratory-based surveillance, 2012-2015. J Med Virol 2017; 89:1700-1706. [PMID: 27943329 PMCID: PMC7166983 DOI: 10.1002/jmv.24751] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 10/18/2016] [Accepted: 11/28/2016] [Indexed: 12/31/2022]
Abstract
Acute respiratory infections (ARIs), with viral pathogens as the major contributors, are the most common illnesses worldwide, and increase the morbidity and mortality among the elderly population. The clinical and pathological features of elderly people with ARIs need to be identified for disease intervention. From January 1, 2012 through December 31, 2015, respiratory specimens from patients above 60 years old with ARIs were collected from the outpatient and inpatient settings of six sentinel hospitals in Pudong New Area. Each specimen was tested via multiplex polymerase chain reaction (PCR) for eight target viral etiologies including influenza, human rhinovirus (HRV), human para‐influenza virus (PIV), adenovirus (ADV), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), human coronavirus (hCoVs), and human bocavirus (hBoV). A total of 967 elderly patients with ARIs were enrolled, including 589 (60.91%) males, and the median age was 73 years old. 306 (31.64%) patients were tested positive for any one of the eight viruses, including 276 single infections and 30 co‐infections. Influenza was the predominant virus (14.17%, 137/967), detected from 21.35% (76/356) of the outpatients and 9.98% (61/611) of the inpatients. Influenza infections presented two annual seasonal peaks during winter and summer. Compared with non‐influenza patients, those with influenza were more likely to have fever, cough, sore throat, and fatigue. This study identified influenza as the leading viral pathogen among elderly with ARIs, and two seasonal epidemic peaks were observed in Shanghai. An influenza vaccination strategy needs to be advocated for the elderly population.
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Affiliation(s)
- Chuchu Ye
- School of Public Health, Fudan University, Shanghai, China.,Research Base of Key Laboratory of Surveillance and Early-Warning on Infectious Disease in China, CDC, Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Weiping Zhu
- Research Base of Key Laboratory of Surveillance and Early-Warning on Infectious Disease in China, CDC, Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Jianxing Yu
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhongjie Li
- Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yifei Fu
- Research Base of Key Laboratory of Surveillance and Early-Warning on Infectious Disease in China, CDC, Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Yajia Lan
- Research Base of Key Laboratory of Surveillance and Early-Warning on Infectious Disease in China, CDC, West China School of Public Health, Sichuan University, Chengdu, China
| | - Shengjie Lai
- Key Laboratory of Surveillance and Early-Warning on Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China.,Department of Geography and Environment, University of Southampton, Southampton, UK
| | - Yuanping Wang
- Research Base of Key Laboratory of Surveillance and Early-Warning on Infectious Disease in China, CDC, Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Lifeng Pan
- Research Base of Key Laboratory of Surveillance and Early-Warning on Infectious Disease in China, CDC, Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Qiao Sun
- Research Base of Key Laboratory of Surveillance and Early-Warning on Infectious Disease in China, CDC, Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, China
| | - Genming Zhao
- School of Public Health, Fudan University, Shanghai, China
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16
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Shapiro D, Bodinayake CK, Nagahawatte A, Devasiri V, Kurukulasooriya R, Hsiang J, Nicholson B, De Silva AD, Østbye T, Reller ME, Woods CW, Tillekeratne LG. Burden and Seasonality of Viral Acute Respiratory Tract Infections among Outpatients in Southern Sri Lanka. Am J Trop Med Hyg 2017; 97:88-96. [PMID: 28719323 PMCID: PMC5508919 DOI: 10.4269/ajtmh.17-0032] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/08/2017] [Indexed: 11/07/2022] Open
Abstract
In tropical and subtropical settings, the epidemiology of viral acute respiratory tract infections varies widely between countries. We determined the etiology, seasonality, and clinical presentation of viral acute respiratory tract infections among outpatients in southern Sri Lanka. From March 2013 to January 2015, we enrolled outpatients presenting with influenza-like illness (ILI). Nasal/nasopharyngeal samples were tested in duplicate using antigen-based rapid influenza testing and multiplex polymerase chain reaction (PCR) for respiratory viruses. Monthly proportion positive was calculated for each virus. Bivariable and multivariable logistic regression were used to identify associations between sociodemographic/clinical information and viral detection. Of 571 subjects, most (470, 82.3%) were ≥ 5 years of age and 53.1% were male. A respiratory virus was detected by PCR in 63.6% (N = 363). Common viral etiologies included influenza (223, 39%), human enterovirus/rhinovirus (HEV/HRV, 14.5%), respiratory syncytial virus (RSV, 4.2%), and human metapneumovirus (hMPV, 3.9%). Both ILI and influenza showed clear seasonal variation, with peaks from March to June each year. RSV and hMPV activity peaked from May to July, whereas HEV/HRV was seen year-round. Patients with respiratory viruses detected were more likely to report pain with breathing (odds ratio [OR] = 2.60, P = 0.003), anorexia (OR = 2.29, P < 0.001), and fatigue (OR = 2.00, P = 0.002) compared with patients with no respiratory viruses detected. ILI showed clear seasonal variation in southern Sri Lanka, with most activity during March to June; peak activity was largely due to influenza. Targeted infection prevention activities such as influenza vaccination in January-February may have a large public health impact in this region.
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Affiliation(s)
- David Shapiro
- Department of Pediatrics, Duke University, Durham, North Carolina
| | | | - Ajith Nagahawatte
- Department of Microbiology, Faculty of Medicine, Ruhuna University, Galle, Sri Lanka
| | - Vasantha Devasiri
- Department of Pediatrics, Faculty of Medicine, Ruhuna University, Galle, Sri Lanka
| | | | - Jeremy Hsiang
- Durham Veterans Affairs Medical Center, Durham, North Carolina
| | | | | | - Truls Østbye
- Duke Global Health Institute, Durham, North Carolina
- Department of Community and Family Medicine, Duke University, Durham, North Carolina
| | - Megan E. Reller
- Department of Medicine, Duke University, Durham, North Carolina
| | - Christopher W. Woods
- Duke Global Health Institute, Durham, North Carolina
- Department of Medicine, Duke University, Durham, North Carolina
| | - L. Gayani Tillekeratne
- Duke Global Health Institute, Durham, North Carolina
- Department of Medicine, Duke University, Durham, North Carolina
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17
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Multiple Viral Infection Detected from Influenza-Like Illness Cases in Indonesia. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9541619. [PMID: 28232948 PMCID: PMC5292373 DOI: 10.1155/2017/9541619] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/22/2016] [Accepted: 12/13/2016] [Indexed: 01/30/2023]
Abstract
Influenza is one of the common etiologies of the upper respiratory tract infection (URTI). However, influenza virus only contributes about 20 percent of influenza-like illness patients. The aim of the study is to investigate the other viral etiologies from ILI cases in Indonesia. Of the 334 samples, 266 samples (78%) were positive at least for one virus, including 107 (42%) cases of multiple infections. Influenza virus is the most detected virus. The most frequent combination of viruses identified was adenovirus and human rhinovirus. This recent study demonstrated high detection rate of several respiratory viruses from ILI cases in Indonesia. Further studies to determine the relationship between viruses and clinical features are needed to improve respiratory disease control program.
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18
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Daughton AR, Velappan N, Abeyta E, Priedhorsky R, Deshpande A. Novel Use of Flu Surveillance Data: Evaluating Potential of Sentinel Populations for Early Detection of Influenza Outbreaks. PLoS One 2016; 11:e0158330. [PMID: 27391232 PMCID: PMC4938434 DOI: 10.1371/journal.pone.0158330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/14/2016] [Indexed: 11/18/2022] Open
Abstract
Influenza causes significant morbidity and mortality each year, with 2-8% of weekly outpatient visits around the United States for influenza-like-illness (ILI) during the peak of the season. Effective use of existing flu surveillance data allows officials to understand and predict current flu outbreaks and can contribute to reductions in influenza morbidity and mortality. Previous work used the 2009-2010 influenza season to investigate the possibility of using existing military and civilian surveillance systems to improve early detection of flu outbreaks. Results suggested that civilian surveillance could help predict outbreak trajectory in local military installations. To further test that hypothesis, we compare pairs of civilian and military outbreaks in seven locations between 2000 and 2013. We find no predictive relationship between outbreak peaks or time series of paired outbreaks. This larger study does not find evidence to support the hypothesis that civilian data can be used as sentinel surveillance for military installations. We additionally investigate the effect of modifying the ILI case definition between the standard Department of Defense definition, a more specific definition proposed in literature, and confirmed Influenza A. We find that case definition heavily impacts results. This study thus highlights the importance of careful selection of case definition, and appropriate consideration of case definition in the interpretation of results.
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Affiliation(s)
- Ashlynn R. Daughton
- Analytics, Intelligence and Technology Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
- * E-mail: (ARD); (AD)
| | - Nileena Velappan
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Esteban Abeyta
- Analytics, Intelligence and Technology Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Reid Priedhorsky
- High Performance Computing Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Alina Deshpande
- Analytics, Intelligence and Technology Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
- * E-mail: (ARD); (AD)
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19
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Epidemiological and clinical characteristics of respiratory viral infections in children in Shanghai, China. Arch Virol 2016; 161:1907-13. [PMID: 27138548 PMCID: PMC7086729 DOI: 10.1007/s00705-016-2866-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 04/14/2016] [Indexed: 12/21/2022]
Abstract
Acute respiratory tract infections (ARTIs) due to various viruses are not only the most common causes of upper and lower respiratory infection but are also major causes of morbidity and mortality in children. In this study, we investigated the prevalence and clinical characteristics of children with virus-related ARTIs and determined the spectrum of respiratory viruses and their correlation with meteorological variables in Jiading District, Shanghai, China. Nasopharyngeal swabs from 2819 children with ARTIs were collected from August 2011 to December 2014, and used for detection of respiratory viruses by multiplex RT-PCR. Seventeen respiratory viruses were detected among 691 (24.5 %) of 2819 patients. The highest prevalence of respiratory viruses was detected in the age group of less than 1 year (29.0 %), and the prevalence decreased with age. This suggests that children less than one year old are the most susceptible to infection. Influenza virus (IFV) was the most frequently detected virus (5.8 %), followed by parainfluenza virus (PIV) (5.7 %), enterovirus (EV) (4.3 %), and respiratory syncytial virus (RSV) (3.6 %). Statistical analysis showed that epidemics of IFV, PIV and EV had distinct seasonal variations. Mean monthly temperature appeared to be the only meteorological factor associated with IFV and PIV infection. These findings will provide valuable information for decision-making, prevention and treatment of ARTIs in children.
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20
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Kwok CS, Aslam S, Kontopantelis E, Myint PK, Zaman MJS, Buchan I, Loke YK, Mamas MA. Influenza, influenza-like symptoms and their association with cardiovascular risks: a systematic review and meta-analysis of observational studies. Int J Clin Pract 2015; 69:928-37. [PMID: 25940136 PMCID: PMC7165588 DOI: 10.1111/ijcp.12646] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
AIMS To synthesise the evidence relating influenza and influenza-like symptoms to the risks of myocardial infarction (MI), heart failure (HF) and stroke. METHODS We conducted a systematic review and meta-analysis of the evidence relating influenza and influenza-like symptoms to the risks of MI, HF and stroke. We systematically searched all MEDLINE and EMBASE entries up to August 2014 for studies of influenza vs. the cardiovascular outcomes above. We conducted random effects meta-analysis using inverse variance method for pooled odds ratios (OR) and evaluated statistical heterogeneity using the I(2) statistic. RESULTS We identified 12 studies with a total of 84,003 participants. The pooled OR for risk of MI vs. influenza (serologically confirmed) was 1.27 (95% CI, confidence interval 0.54-2.95), I(2) = 47%, which was significant for the only study that adjusted for confounders (OR 5.50, 95% CI 1.31-23.13). The pooled OR for risk of MI vs. influenza-like symptoms was 2.17 (95% CI 1.68-2.80), I(2) = 0%, which was significant for both unadjusted (OR 2.23, 95% CI 1.65-3.01, five studies) and adjusted studies (OR 2.01, 95% CI 1.24-3.27, two studies). We found one study that evaluated stroke risk, one study in patients with HF, and one that evaluated mortality from MI - all of these studies suggested increased risks of events with influenza-like symptoms. CONCLUSIONS There is an association between influenza-like illness and cardiovascular events, but the relationship is less clear with serologically diagnosed influenza. We recommend renewed efforts to apply current clinical guidelines and maximise the uptake of annual influenza immunisation among patients with cardiovascular diseases, to decrease their risks of MI and stroke.
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Affiliation(s)
- C S Kwok
- Cardiovascular Research Group, Institute of Cardiovascular Sciences, University of Manchester, Manchester, UK
| | - S Aslam
- Central Manchester Foundation Trust, Manchester, UK
| | - E Kontopantelis
- Centre for Health Informatics, Institute of Population Health, University of Manchester, Manchester, UK
| | - P K Myint
- Institute of Applied Health Sciences, University of Aberdeen, Aberdeen, UK
| | - M J S Zaman
- Department of Cardiology, James Paget University Hospital, Gorleston-on-Sea, UK
| | - I Buchan
- Centre for Health Informatics, Institute of Population Health, University of Manchester, Manchester, UK
| | - Y K Loke
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - M A Mamas
- Cardiovascular Research Group, Institute of Cardiovascular Sciences, University of Manchester, Manchester, UK
- Keele Cardiovascular Research Group, University of Keele, Stoke-on-Trent, UK
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21
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Otomaru H, Kamigaki T, Tamaki R, Opinion J, Santo A, Daya E, Okamoto M, Saito M, Tallo V, Lupisan S, Suzuki A, Oshitani H. Influenza and other respiratory viruses detected by influenza-like illness surveillance in Leyte Island, the Philippines, 2010-2013. PLoS One 2015; 10:e0123755. [PMID: 25893441 PMCID: PMC4404362 DOI: 10.1371/journal.pone.0123755] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 02/23/2015] [Indexed: 01/06/2023] Open
Abstract
This study aimed to determine the role of influenza-like illness (ILI) surveillance conducted on Leyte Island, the Philippines, including involvement of other respiratory viruses, from 2010 to 2013. ILI surveillance was conducted from January 2010 to March 2013 with 3 sentinel sites located in Tacloban city, Palo and Tanauan of Leyte Island. ILI was defined as fever ≥38°C or feverish feeling and either cough or running nose in a patient of any age. Influenza virus and other 5 respiratory viruses were searched. A total of 5,550 ILI cases visited the 3 sites and specimens were collected from 2,031 (36.6%) cases. Among the cases sampled, 1,637 (75.6%) were children aged <5 years. 874 (43.0%) cases were positive for at least one of the respiratory viruses tested. Influenza virus and respiratory syncytial virus (RSV) were predominantly detected (both were 25.7%) followed by human rhinovirus (HRV) (17.5%). The age distributions were significantly different between those who were positive for influenza, HRV, and RSV. ILI cases were reported throughout the year and influenza virus was co-detected with those viruses on approximately half of the weeks of study period (RSV in 60.5% and HRV 47.4%). In terms of clinical manifestations, only the rates of headache and sore throat were significantly higher in influenza positive cases than cases positive to other viruses. In conclusion, syndromic ILI surveillance in this area is difficult to detect the start of influenza epidemic without laboratory confirmation which requires huge resources. Age was an important factor that affected positive rates of influenza and other respiratory viruses. Involvement of older age children may be useful to detect influenza more effectively.
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Affiliation(s)
- Hirono Otomaru
- Department of Virology, Tohoku University School of Medicine, Sendai, Japan
| | - Taro Kamigaki
- Department of Virology, Tohoku University School of Medicine, Sendai, Japan
- * E-mail:
| | - Raita Tamaki
- Department of Virology, Tohoku University School of Medicine, Sendai, Japan
| | - Jamie Opinion
- Tacloban City Health Office, Tacloban City, the Philippines
| | - Arlene Santo
- Tanauan Rural Health Unit, Tanauan, the Philippines
| | - Edgard Daya
- Leyte Provincial Health Office, Palo, the Philippines
| | - Michiko Okamoto
- Department of Virology, Tohoku University School of Medicine, Sendai, Japan
| | - Mariko Saito
- Department of Virology, Tohoku University School of Medicine, Sendai, Japan
- Tohoku-RITM Research Center for Emerging and Reemerging Infections, Muntinlupa City, the Philippines
| | - Veronica Tallo
- Research Institute for Tropical Medicine, Muntinlupa City, the Philippines
| | - Soccoro Lupisan
- Research Institute for Tropical Medicine, Muntinlupa City, the Philippines
| | - Akira Suzuki
- Virus Research Center, Clinical Research Division, Sendai Medical Center, Sendai, Japan
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University School of Medicine, Sendai, Japan
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22
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The clinical and etiological characteristics of influenza-like illness (ILI) in outpatients in Shanghai, China, 2011 to 2013. PLoS One 2015; 10:e0119513. [PMID: 25822885 PMCID: PMC4379014 DOI: 10.1371/journal.pone.0119513] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 01/30/2015] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Clinical and etiological characteristics of influenza-like illness (ILI) in outpatients is poorly understood in the southern temperate region of China. We conducted laboratory-based surveillance of viral etiology for ILI outpatients in Shanghai from January 2011 to December 2013. MATERIALS AND METHODS Clinical and epidemiological data from ILI outpatients, both children and adults, were collected. A total of 1970 nasopharyngeal swabs were collected and tested for 12 respiratory viruses using multiplex RT-PCR, and the data were analyzed anonymously. RESULTS All 12 respiratory viruses were detected in the specimens. At least one virus was detected in 32.4% of 1970 specimens analyzed, with 1.1% showing co-infections. The most frequently detected agents were influenza A (11.7%), influenza B (9.6%), and rhinoviruses (3.1%).Other viruses were present at a frequency less than 3.0%. We observed a winter peak in the detection rate in ILI patients during 3 years of surveillance and a summer peak in 2012. HCoV, HADV, and HMPV were detected more frequently in children than in adults. Patients infected with influenza virus experienced higher temperatures, more coughs, running noses, headaches and fatigue than patients infected with other viruses and virus-free patients (p<0.001). CONCLUSIONS The spectrum, seasonality, age distribution and clinical associations of respiratory virus infections in children and adults with influenza-like illness were analyzed in this study for the first time. To a certain extent, the findings can provide baseline data for evaluating the burden of respiratory virus infection in children and adults in Shanghai. It will also provide clinicians with helpful information about the etiological patterns of outpatients presenting with complaints of acute respiratory syndrome, but further studies should be conducted, and longer-term laboratory-based surveillance would give a better picture of the etiology of ILI.
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Cui B, Zhang D, Pan H, Zhang F, Farrar J, Law F, van Doorn HR, Wu B, Ba-Thein W. Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China. BMC Infect Dis 2015; 15:124. [PMID: 25884513 PMCID: PMC4365542 DOI: 10.1186/s12879-015-0863-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 03/02/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Acute respiratory infections (ARIs) are common in children and mostly caused by viruses, but the significance of the detection of multiple viruses in ARIs is unclear. This study investigated 14 respiratory viruses in ARIs among children and associated meteorological factors in Shantou, southern China. METHODS Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses--influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV)--by multiplex real-time PCR. RESULTS We identified at least one virus in 82.3% (884/1,074) and multiple viruses in 38.6% (415/1,074) of patients. EV and HRV were the most frequently detected single viruses (42.3%, 374/884 and 39.9%, 353/884 respectively) and co-detected pair (23.1%, 96/415). Overlapping seasonal trends of viruses were recorded over the year, with dual peaks for EV and single peaks for the others. By logistic regression analysis, EV was positively associated with the average temperature and humidity, hCoV, and PIV4, but negatively with HRV, PIV3, and hBoV. HRV was inversely associated with EV and PIV3. CONCLUSIONS This study reports high viral detection and co-detection rates in pediatric ARI cases mainly due to EV and HRV. Many viruses circulated throughout the year with similar seasonal trends in association with temperature, humidity, and wind velocity. Statistically significant associations were present among the viruses. Understanding the polyviral etiology and viral interactions in the cases with multiple viruses warrants further studies.
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Affiliation(s)
- Binglin Cui
- Pediatric Department, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - Dangui Zhang
- The Research Center of Translational Medicine, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - Hui Pan
- Shantou-Oxford Clinical Research Unit, Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - Fan Zhang
- Oncology Research Laboratory, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Viet Nam.
| | - Frieda Law
- Consultant Office, Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Viet Nam.
| | - Beiyan Wu
- Pediatric Department, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - William Ba-Thein
- Shantou-Oxford Clinical Research Unit, Shantou University Medical College, Shantou, Guangdong, P.R. China.
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, Guangdong, 515041, P.R. China.
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Minodier L, Arena C, Heuze G, Ruello M, Amoros JP, Souty C, Varesi L, Falchi A. Epidemiology and viral etiology of the influenza-like illness in corsica during the 2012-2013 Winter: an analysis of several sentinel surveillance systems. PLoS One 2014; 9:e100388. [PMID: 24959929 PMCID: PMC4069071 DOI: 10.1371/journal.pone.0100388] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 05/26/2014] [Indexed: 11/19/2022] Open
Abstract
Influenza-like illness (ILI) surveillance is important to identify circulating and emerging/reemerging strains and unusual epidemiological trends. The present study aimed to give an accurate picture of the 2012-2013 ILI outbreak in Corsica by combining data from several surveillance systems: general practice, emergency general practice, hospital emergency units, intensive care units, and nursing homes. Twenty-eight respiratory viruses were retrospectively investigated from patients in general practice with ILI. Sequence analysis of the genetic changes in the hemagglutinin gene of influenza viruses (A(H1N1)pdm2009, A(H3N2) and B) was performed. The trends in ILI/influenza consultation rates and the relative illness ratios (RIRs) of having an ILI consultation were estimated by age group for the different surveillance systems analyzed. Of the 182 ILI patients enrolled by general practitioners, 57.7% tested positive for influenza viruses. Phylogenetic analyses suggested a genetic drift for influenza B and A(H3N2) viruses. The ILI/influenza surveillance systems showed similar trends and were well correlated. In accordance with virological data, the RIRs of having an ILI consultation were highest among the young (<15 years old) and decreased with age. No clusters of acute respiratory illness were declared by the sentinel nursing homes. This study is noteworthy in that it is the first extensive description of the 2012-2013 ILI outbreak in Corsica as monitored through several surveillance systems. To improve ILI surveillance in Corsica, a consortium that links together the complementary regional surveillance ILI systems described here is being implemented.
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Affiliation(s)
- Laëtitia Minodier
- EA7310, Laboratoire de Virologie, Université de Corse, Institut national de la Santé et de la Recherche Médicale, Corte, France
| | - Christophe Arena
- EA7310, Laboratoire de Virologie, Université de Corse, Institut national de la Santé et de la Recherche Médicale, Corte, France
- Observatoire régional de la Santé de Corse, Ajaccio, France
| | - Guillaume Heuze
- Cellule de l'Institut national de Veille Sanitaire en région, Ajaccio, France
| | - Marc Ruello
- Cellule de l'Institut national de Veille Sanitaire en région, Ajaccio, France
| | - Jean Pierre Amoros
- EA7310, Laboratoire de Virologie, Université de Corse, Institut national de la Santé et de la Recherche Médicale, Corte, France
| | - Cécile Souty
- Sorbonne Universités Pierre et Marie Curie, Paris 06, UMRS 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
- Institut national de la Santé et de la Recherche Médicale, UMRS 1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France
| | - Laurent Varesi
- EA7310, Laboratoire de Virologie, Université de Corse, Institut national de la Santé et de la Recherche Médicale, Corte, France
| | - Alessandra Falchi
- EA7310, Laboratoire de Virologie, Université de Corse, Institut national de la Santé et de la Recherche Médicale, Corte, France
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Feng L, Li Z, Zhao S, Nair H, Lai S, Xu W, Li M, Wu J, Ren L, Liu W, Yuan Z, Chen Y, Wang X, Zhao Z, Zhang H, Li F, Ye X, Li S, Feikin D, Yu H, Yang W. Viral etiologies of hospitalized acute lower respiratory infection patients in China, 2009-2013. PLoS One 2014; 9:e99419. [PMID: 24945280 PMCID: PMC4063718 DOI: 10.1371/journal.pone.0099419] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 05/14/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Acute lower respiratory infections (ALRIs) are an important cause of acute illnesses and mortality worldwide and in China. However, a large-scale study on the prevalence of viral infections across multiple provinces and seasons has not been previously reported from China. Here, we aimed to identify the viral etiologies associated with ALRIs from 22 Chinese provinces. METHODS AND FINDINGS Active surveillance for hospitalized ALRI patients in 108 sentinel hospitals in 24 provinces of China was conducted from January 2009-September 2013. We enrolled hospitalized all-age patients with ALRI, and collected respiratory specimens, blood or serum collected for diagnostic testing for respiratory syncytial virus (RSV), human influenza virus, adenoviruses (ADV), human parainfluenza virus (PIV), human metapneumovirus (hMPV), human coronavirus (hCoV) and human bocavirus (hBoV). We included 28,369 ALRI patients from 81 (of the 108) sentinel hospitals in 22 (of the 24) provinces, and 10,387 (36.6%) were positive for at least one etiology. The most frequently detected virus was RSV (9.9%), followed by influenza (6.6%), PIV (4.8%), ADV (3.4%), hBoV (1.9), hMPV (1.5%) and hCoV (1.4%). Co-detections were found in 7.2% of patients. RSV was the most common etiology (17.0%) in young children aged <2 years. Influenza viruses were the main cause of the ALRIs in adults and elderly. PIV, hBoV, hMPV and ADV infections were more frequent in children, while hCoV infection was distributed evenly in all-age. There were clear seasonal peaks for RSV, influenza, PIV, hBoV and hMPV infections. CONCLUSIONS Our findings could serve as robust evidence for public health authorities in drawing up further plans to prevent and control ALRIs associated with viral pathogens. RSV is common in young children and prevention measures could have large public health impact. Influenza was most common in adults and influenza vaccination should be implemented on a wider scale in China.
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Affiliation(s)
- Luzhao Feng
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Zhongjie Li
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Shiwen Zhao
- Yunnan Provincial Center for Disease Control and Prevention, Kunming, China
| | - Harish Nair
- Centre for Population Health Sciences, Global Health Academy, The University of Edinburgh, Edinburgh, United Kingdom
- Public Health Foundation of India, New Delhi, India
| | - Shengjie Lai
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Wenbo Xu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengfeng Li
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Jianguo Wu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Lili Ren
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wei Liu
- Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | | | - Yu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xinhua Wang
- Gansu Provincial Center for Disease Control and Prevention, Lanzhou, China
| | - Zhuo Zhao
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang, China
| | - Honglong Zhang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Fu Li
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Xianfei Ye
- Shanghai Public Health Clinical Center, Shanghai, China
| | - Sa Li
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China
| | - Daniel Feikin
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Hongjie Yu
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China
- * E-mail: (WY); (HY)
| | - Weizhong Yang
- Division of Infectious Disease, Key Laboratory of Surveillance and Early-warning on Infectious Disease, Chinese Centre for Disease Control and Prevention, Beijing, China
- * E-mail: (WY); (HY)
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Tan XQ, Zhao X, Lee VJ, Loh JP, Tan BH, Koh WHV, Ng SH, Chen MIC, Cook AR. Respiratory viral pathogens among Singapore military servicemen 2009-2012: epidemiology and clinical characteristics. BMC Infect Dis 2014; 14:204. [PMID: 24735158 PMCID: PMC4006965 DOI: 10.1186/1471-2334-14-204] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 04/08/2014] [Indexed: 11/25/2022] Open
Abstract
Background Few studies have comprehensively described tropical respiratory disease surveillance in military populations. There is also a lack of studies comparing clinical characteristics of the non-influenza pathogens with influenza and amongst themselves. Methods From May 2009 through October 2012, 7733 consenting cases of febrile respiratory illness (FRI) (temperature [greater than or equal to]37.5degreesC with cough or sorethroat) and controls in the Singapore military had clinical data and nasal washes collected prospectively. Nasal washes underwent multiplex PCR, and the analysis was limited to viral mono-infections. Results 49% of cases tested positive for at least one virus, of whom 10% had multiple infections. 53% of the FRI cases fulfilled the definition of influenza-like illness (ILI), of whom 52% were positive for at least one virus. The most frequent etiologies for mono-infections among FRI cases were Influenza A(H1N1)pdm09 (13%), Influenza B (13%) and coxsackevirus (9%). The sensitivity, specificity, positive predictive value and negative predictive value of ILI for influenza among FRI cases were 72%, 48%, 40% and 69% respectively. On logistic regression, there were marked differences in the prevalence of different symptoms and signs between viruses with fever more prevalent amongst influenza and adenovirus infections than other viruses. Conclusion There are multiple viral etiologies for FRI and ILI with differing clinical symptoms in the Singapore military. Influenza and coxsackevirus were the most common etiology for FRI, while influenza and adenoviruses displayed the most febrile symptoms. Further studies should explore these differences and possible interventions.
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Affiliation(s)
| | | | - Vernon J Lee
- Biodefence Centre, Ministry of Defence, Singapore, Singapore.
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Dia N, Richard V, Kiori D, Cisse EHAK, Sarr FD, Faye A, Goudiaby DG, Diop OM, Niang MN. Respiratory viruses associated with patients older than 50 years presenting with ILI in Senegal, 2009 to 2011. BMC Infect Dis 2014; 14:189. [PMID: 24712515 PMCID: PMC4020602 DOI: 10.1186/1471-2334-14-189] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 04/03/2014] [Indexed: 11/30/2022] Open
Abstract
Background In Africa, especially in West Africa, studies about the prevalence and diversity of respiratory viruses (influenza and others) in elderly people are largely lacking. In studies done elsewhere, it is well established that older people, when compared with younger adults, are at greater risk of significant morbidity and mortality from complications arising from influenza. The main aim of this study was to determine the prevalence and the diversity of respiratory viruses associated with ILI cases in adults over 50 years old in Senegal. Methods The recruitment period of this study was from January 2009 to December 2011. 232 patients aged 50 years and above presenting ILI cases were enrolled. Nasal-pharyngeal and/or oral pharyngeal swabs were collected from patients. RNA was extracted from 200 μl of each sample followed by a two-step real-time RT-PCR. The Anyplex™ II RV16 Detection kit was used for viral detection. The kit enabled the simultaneous detection of the presence of 16 respiratory viruses. Results 150 viruses were detected: influenza viruses (44.7%) and rhinoviruses (26.7%) were the most prevalent. We detected 13 human parainfluenza viruses (8.7%), 7 human respiratory syncytial viruses (4.7%), 6 coronaviruses (4%), 5 human metapneumoviruses (3.3%), 5 human adenoviruses (3.3%) and 1 human bocavirus (0.7%). 14 cases (6%) of dual virus infections and one triple viral detection case were encountered. 56 (56.6%) viruses detected were found in the 50-64 year old age group, 59 (76.6%; P < 0.001) from 65–74 year old age group and 35 (62.5%) were detected in the ≥75 year old age group. The viral co-infections were more frequent in the 65-74 age group (9/15). Conclusions This pilot study demonstrates a variety of respiratory viruses in the elderly. It also highlights a high prevalence of these viruses in this age group. We speculate from these results that the impact of respiratory viruses other than influenza on the elderly has been considerably underestimated. A more exhaustive study seems necessary in order to provide a more complete picture of the burden of respiratory viruses on morbidity among adults over 50 years old in the sub-Saharan context.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Mbayame N Niang
- Unit of Medical Virology, Institut Pasteur de Dakar, Unité de Virologie Médicale, Dakar, BP; 220, Dakar, Senegal.
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Viral etiology of influenza-like illnesses in Huizhou, China, from 2011 to 2013. Arch Virol 2014; 159:2003-10. [PMID: 24610554 PMCID: PMC7086676 DOI: 10.1007/s00705-014-2035-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 02/22/2014] [Indexed: 01/17/2023]
Abstract
Little information is available on the etiology and prevalence of viruses other than influenza viruses causing influenza-like illnesses (ILIs) in China. This study was conducted for simultaneous detection and identification of 14 respiratory viruses in Huizhou using real-time PCR. In total, viruses were detected in 48.66 % of ILI patient samples, in which influenza virus (19.98 %) was the most commonly detected, followed by rhinovirus (7.46 %), human coronaviruses (3.63 %), human metapneumovirus (3.06 %), parainfluenza virus (3.06 %), respiratory syncytial virus (2.39 %), adenovirus (2.29 %), and human bocavirus (1.43 %). Co-infections occurred in 5.35 % of all tested specimens and 11.00 % (56/509) of infected patients. Children under 5 years and adults older than 60 years were more likely to have one or more detectable viruses associated with their ILI (OR=1.75, 95 % CI: 1.37; 2.23). Influenza virus was detected during each month of each year, and increased viral activity was observed in 2013. Infections with adenovirus and human metapneumovirus had characteristic seasonal patterns. No significant differences were found in positive the rate between the gender groups, while significantly differences in positive rate were found among the different age groups (P-value<0.001). This study confirmed that multiple respiratory viruses may circulate concurrently in the population and play an important role in the etiology of ILI. The most frequent symptoms associated with respiratory viruses were sore throat, rhinorrhea and headache. This information needs to be considered by clinicians when treating patients presenting with ILI, and it could serve as a reference for government officers when designing and implementing effective intervention plans.
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Dominguez SR, Shrivastava S, Berglund A, Qian Z, Góes LGB, Halpin RA, Fedorova N, Ransier A, Weston PA, Durigon EL, Jerez JA, Robinson CC, Town CD, Holmes KV. Isolation, propagation, genome analysis and epidemiology of HKU1 betacoronaviruses. J Gen Virol 2014; 95:836-848. [PMID: 24394697 DOI: 10.1099/vir.0.059832-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
From 1 January 2009 to 31 May 2013, 15 287 respiratory specimens submitted to the Clinical Virology Laboratory at the Children's Hospital Colorado were tested for human coronavirus RNA by reverse transcription-PCR. Human coronaviruses HKU1, OC43, 229E and NL63 co-circulated during each of the respiratory seasons but with significant year-to-year variability, and cumulatively accounted for 7.4-15.6 % of all samples tested during the months of peak activity. A total of 79 (0.5 % prevalence) specimens were positive for human betacoronavirus HKU1 RNA. Genotypes HKU1 A and B were both isolated from clinical specimens and propagated on primary human tracheal-bronchial epithelial cells cultured at the air-liquid interface and were neutralized in vitro by human intravenous immunoglobulin and by polyclonal rabbit antibodies to the spike glycoprotein of HKU1. Phylogenetic analysis of the deduced amino acid sequences of seven full-length genomes of Colorado HKU1 viruses and the spike glycoproteins from four additional HKU1 viruses from Colorado and three from Brazil demonstrated remarkable conservation of these sequences with genotypes circulating in Hong Kong and France. Within genotype A, all but one of the Colorado HKU1 sequences formed a unique subclade defined by three amino acid substitutions (W197F, F613Y and S752F) in the spike glycoprotein and exhibited a unique signature in the acidic tandem repeat in the N-terminal region of the nsp3 subdomain. Elucidating the function of and mechanisms responsible for the formation of these varying tandem repeats will increase our understanding of the replication process and pathogenicity of HKU1 and potentially of other coronaviruses.
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Affiliation(s)
- Samuel R Dominguez
- Departments of Microbiology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA.,Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Susmita Shrivastava
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Andrew Berglund
- Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Zhaohui Qian
- Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Luiz Gustavo Bentim Góes
- Interdisciplinary Graduate Program in Biotechnology, University of São Paulo, Av Prof. Lineu Prestes, 2415, ICB-III, Cidade Universitária, CEP: 05508-900, São Paulo, SP - Brazil.,J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Rebecca A Halpin
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Nadia Fedorova
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Amy Ransier
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Philip A Weston
- Departments of Pediatrics, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
| | - Edison Luiz Durigon
- Interdisciplinary Graduate Program in Biotechnology, University of São Paulo, Av Prof. Lineu Prestes, 2415, ICB-III, Cidade Universitária, CEP: 05508-900, São Paulo, SP - Brazil.,J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - José Antonio Jerez
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av Prof. Lineu Prestes 1374, ICB-II, Cidade Universitária, CEP: 05580-900, São Paulo, SP - Brazil.,J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA
| | - Christine C Robinson
- Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva, 87, Cidade Universitária, CEP: 05508-270, Sao Paulo, SP - Brazil
| | - Christopher D Town
- Department of Pathology and Clinical Medicine, Children's Hospital Colorado, 13123 E 16th Ave, Aurora, CO 80045, USA
| | - Kathryn V Holmes
- Departments of Microbiology, University of Colorado School of Medicine, Anschutz Medical Campus, 12800 E 19th Ave, Room P18-9403B, Aurora, CO 80045, USA
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Kono J, Jonduo MH, Omena M, Siba PM, Horwood PF. Viruses associated with influenza-like-illnesses in Papua New Guinea, 2010. J Med Virol 2013; 86:899-904. [PMID: 24136362 PMCID: PMC7166351 DOI: 10.1002/jmv.23786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2013] [Indexed: 12/31/2022]
Abstract
Influenza‐like‐illness can be caused by a wide range of respiratory viruses. The etiology of influenza‐like‐illness in developing countries such as Papua New Guinea is poorly understood. The etiological agents associated with influenza‐like‐illness were investigated retrospectively for 300 nasopharyngeal swabs received by the Papua New Guinea National Influenza Centre in 2010. Real‐time PCR/RT‐PCR methods were used for the detection of 13 respiratory viruses. Patients with influenza‐like‐illness were identified according to the World Health Organization case definition: sudden onset of fever (>38°C), with cough and/or sore throat, in the absence of other diagnoses. At least one viral respiratory pathogen was detected in 66.3% of the samples tested. Rhinoviruses (17.0%), influenza A (16.7%), and influenza B (12.7%) were the pathogens detected most frequently. Children <5 years of age presented with a significantly higher rate of at least one viral pathogen and a significantly higher rate of co‐infections with multiple viruses, when compared to all other patients >5 years of age. Influenza B, adenovirus, and respiratory syncytial virus were all detected at significantly higher rates in children <5 years of age. This study confirmed that multiple respiratory viruses are circulating and contributing to the presentation of influenza‐like‐illness in Papua New Guinea. J. Med. Virol. 86:899–904, 2014. © 2013 Wiley Periodicals, Inc.
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Affiliation(s)
- Jacinta Kono
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
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